diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib
index c20f0dab..a908e683 100644
--- a/_bibliography/citations-eu.bib
+++ b/_bibliography/citations-eu.bib
@@ -2406,6 +2406,22 @@ @article{de_andrade_whole_2023
  year = {2023}
 }
 
+@article{de_azevedo_genomic_2024,
+ author = {de Azevedo, Bruna Luiza and Queiroz, Victória Fulgêncio and de Aquino, Isabella Luiza Martins and Machado, Talita Bastos and de Assis, Felipe Lopes and Reis, Erik and Araújo Júnior, João Pessoa and Ullmann, Leila Sabrina and Colson, Philippe and Greub, Gilbert and Aylward, Frank and Rodrigues, Rodrigo Araújo Lima and Abrahão, Jônatas Santos},
+ doi = {10.1128/jvi.00513-24},
+ journal = {Journal of Virology},
+ keywords = {{\textgreater}UseGalaxy.eu},
+ month = {May},
+ note = {Publisher: American Society for Microbiology},
+ number = {0},
+ pages = {e00513--24},
+ title = {The genomic and phylogenetic analysis of {Marseillevirus} cajuinensis raises questions about the evolution of {Marseilleviridae} lineages and their taxonomical organization},
+ url = {https://journals.asm.org/doi/full/10.1128/jvi.00513-24},
+ urldate = {2024-06-07},
+ volume = {0},
+ year = {2024}
+}
+
 @article{de_jesus_bertani_whole_2023,
  abstract = {This study analyzes the genomic findings of the first report of Salmonella isolate carrying the blaCTX-M-55 gene, recovered from a bacteremic patient from Brazil. A bacterial isolate positive for the blaCTX-M-55 gene was submitted to antimicrobial susceptibility testing by disk diffusion and epsilometric test. Whole genome sequencing was performed using Illumina technology. Conjugation assay was performed; plasmid sizes determined by S1-PFGE and plasmid content were investigated by hybrid assembly after MinION long reads sequencing. Isolate 288\_18 was identified as sequence type ST13, resistant to ampicillin, cefotaxime, ceftazidime, cefepime, ceftriaxone, and aztreonam. A transferable IncFII plasmid sized approximately 67 kb was found to carry the blaTEM-1 and blaCTX-M-55 in a module consisting of IS26-blaTEM-1B-WbuC-blaCTX-M-55-IS26. In addition, an 117 kb IncI1plasmid was also identified in the 288\_18 isolate, but without additional resistance genes. To the best of our knowledge, this is the first report of blaCTX-M-55 in Salmonella isolated from human infection in Brazil. The occurrence of blaCTX-M-55 in the IncFII epidemic plasmid in a relevant clinical human isolate of Salmonella Agona underscores the urgent need for enhanced and effective continuous surveillance for controlling its dissemination.},
  author = {de Jesus Bertani, Amanda Maria and Vieira, Thais and Reis, Alex Domingos and dos Santos, Carla Adriana and de Almeida, Elisabete Aparecida and Camargo, Carlos Henrique and Casas, Monique Ribeiro Tiba},
@@ -2575,6 +2591,23 @@ @article{deng_lamp_2022
  year = {2022}
 }
 
+@article{deng_massively_2024,
+ abstract = {Performing saturation editing of chromosomal genes will enable the study of genetic variants in situ and facilitate protein and cell engineering. However, current in vivo editing of endogenous genes either lacks flexibility or is limited to discrete codons and short gene fragments, preventing a comprehensive exploration of genotype-phenotype relationships. To enable facile saturation editing of full-length genes, we used a protospacer adjacent motif–relaxed Cas9 variant and homology-directed repair to achieve above 60\% user-defined codon replacement efficiencies in Saccharomyces cerevisiae genome. Coupled with massively parallel DNA design and synthesis, we developed a saturation gene editing method termed CRISPR-Cas9– and homology-directed repair–assisted saturation editing (CHASE) and achieved highly saturated codon swapping of long genomic regions. By applying CHASE to massively edit a well-studied global transcription factor gene, we found known and unreported genetic variants affecting an industrially relevant microbial trait. The user-defined codon editing capability and wide targeting windows of CHASE substantially expand the scope of saturation gene editing.},
+ author = {Deng, Lei and Zhou, Yi-Lian and Cai, Zhenkun and Zhu, Jie and Li, Zenan and Bao, Zehua},
+ doi = {10.1126/sciadv.adj9382},
+ journal = {Science Advances},
+ keywords = {{\textgreater}UseGalaxy.eu},
+ month = {May},
+ note = {Publisher: American Association for the Advancement of Science},
+ number = {20},
+ pages = {eadj9382},
+ title = {Massively parallel {CRISPR}-assisted homologous recombination enables saturation editing of full-length endogenous genes in yeast},
+ url = {https://www.science.org/doi/full/10.1126/sciadv.adj9382},
+ urldate = {2024-06-07},
+ volume = {10},
+ year = {2024}
+}
+
 @misc{depari_long-read_2024,
  abstract = {Abstract* Azadirachta excelsa (Jack) Jacobs, Kayu bawang (Meliaceae) is economically valuable and widely used by the local community in Bengkulu (Sumatra) as carpentry and construction wood because of its good durability class. However, it still has ambiguous scientific multiple names, such as Azadirachta excelsa , Protium javanicum , and Dysoxylum mollissimum. Additional tools such as molecular approaches can be used to verify whether it is true or not that Kayu bawang is scientifically named as Azadirachta excelsa based on previous morphological identification. This study aimed to construct draft chloroplast genome and verify the scientific name based on molecular identification using a single rbc L gene marker. Genomic DNA was extracted from bark cambium originated from three different provenances in Bengkulu, Indonesia, namely TBT-A, TBT-K, and TBT-S. MinION from Oxford Nanopore Technologies was used to sequence the samples following manufacture protocols SQK-LSK109 yielding 481.6 Mb for TBT-A, 597.4 Mb for TBT-K, and 853.1 Mb for TBT-S, respectively. Generated data were assembled and constructed, namely 58,780 bp (14 tRNAs and 47 encoding genes) for TBT-A, 142,139 bp (4 rRNAs, 24 tRNAs, and 78 encoding genes) for TBT-K, and 84,906 bp (24 tRNAs and 53 encoding genes) for TBT-S. Based on the phylogenetic tree, Azadirachta excelsa from three identified tree stands were placed in the same group with other Azadirachta excelsa accessions.},
  author = {Depari, Efratenta Katherina and Wijayanto, Nurheni and Karlinasari, Lina and Rafi, Mohamad and Siregar, Iskandar Zulkarnaen},
@@ -3402,6 +3435,18 @@ @article{fischer_peptide-mediated_2023
  year = {2023}
 }
 
+@article{flores_orozco_evaluation_2024,
+ abstract = {Anaerobic digestion (AD) has shown the potential to reduce the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in animal manures. It stands as a promising option to reduce the risk of the spread of antimicrobial resistance (AMR) due to livestock production and manure applications. However, the underlying mechanisms driving these changes still need to be fully understood. This multidisciplinary study aimed to utilize metagenomics to investigate the molecular and microbial mechanisms associated with the evolution of ARGs and MGEs during the anaerobic digestion (AD) of bovine dairy manure. The research focused on three main aspects: 1) examining the long-term effects of mesophilic (MAD) and thermophilic (TAD) anaerobic digestion on the entire set of ARGs (resistome) and MGEs (mobilome) in manure; 2) comparing the impact of alternative manure treatments, such as storage and solid-liquid separation, on resistomes and mobilomes; 3) identifying microbial groups potentially associated with ARGs and MGEs and microbial shifts potentially driving changes in resistomes and mobilomes. A meta-analysis conducted early in this research informed the primary focus of this research. Two anaerobic digesters operating at mesophilic (36 °C) and the other at thermophilic (55 °C) temperatures were set up, operated, monitored, and studied for 4 and 2 years, respectively. Metagenomics analyses were used to evaluate resistomes, mobilomes, and microbiomes in the mesophilic and thermophilic digesters operating under steady state and in the bovine manure used as substrate. The results indicated that MAD and TAD lowered ARG levels in fresh cattle manure by over 50\% and MGEs by over 65\%. Surprisingly, TAD did not outperform MAD at reducing ARGs and MGEs. Co-occurrence analysis indicated a strong association between microbial groups from the phyla Bacillota (e.g., Jeotgalicoccus, Streptococcus, Enterococcus), Actinomycetota (e.g., Brevibacterium, Rhodococcus), and Pseudomonadota (e.g., Acinetobacter, Comamonas) with these AMR elements. The decline in the abundance of aerobic and facultative anaerobes likely linked to hydrolytic functions was suggested as one of the main drivers of the changes in resistomes and mobilomes. The proximity of toxin-antitoxin systems and transposon structures to specific ARGs (e.g., Erm, tet, Ant(6)-la) was discovered, which could explain the persistence of such ARGs in digestates. The study of the effects of other manure treatments, such as aerobic storage in an open tank and solid-liquid separation, revealed that they are less efficient in reducing ARGs and MGEs from manures than AD. In this study, the high levels of ARGs and genes conferring resistance to heavy metals in a farm operating in an antibiotic-free environment suggested that other antimicrobials, such as foot bathing solutions, may be causing the indirect selection of ARGs. Overall, this research made several contributions to understanding AMR in the context of anaerobic digestion of animal manure that could be extrapolated to other manure treatments. These contributions not only bridge existing gaps in the literature but also pave the way for future research, providing valuable insights that can be used to inform the development of more effective strategies to mitigate the dissemination of AMR associated with manure management, application, and disposal.},
+ author = {Flores Orozco, Daniel},
+ keywords = {{\textgreater}UseGalaxy.eu},
+ language = {eng},
+ month = {May},
+ title = {Evaluation of the long-term effects of anaerobic digestion on bovine manure resistomes and mobilomes and the molecular and microbial mechanisms involved},
+ url = {http://hdl.handle.net/1993/38247},
+ urldate = {2024-06-07},
+ year = {2024}
+}
+
 @article{foll_accessible_2019,
  abstract = {AbstractBackground.  Mass spectrometry imaging is increasingly used in biological and translational research because it has the ability to determine the spatial},
  author = {Föll, Melanie Christine and Moritz, Lennart and Wollmann, Thomas and Stillger, Maren Nicole and Vockert, Niklas and Werner, Martin and Bronsert, Peter and Rohr, Karl and Grüning, Björn Andreas and Schilling, Oliver},
@@ -3841,6 +3886,27 @@ @article{gissi_13-gene_2019
  year = {2019}
 }
 
+@article{giufre_detection_2024,
+ abstract = {Background: Carbapenemase-producing Klebsiella pneumoniae (CP-KP) represents a global threat to public health, with limited antimicrobial therapeutic options. In this study, we analyzed a ceftazidime/avibactam (CAZ-AVI)-resistant K. pneumoniae isolate obtained from a patient previously exposed to CAZ-AVI expressing a novel K. pneumoniae carbapenemase (KPC)-3 variant. Methods: Antimicrobial susceptibility testing was performed using reference broth microdilution. Whole-genome sequencing (WGS) was performed using Illumina and Nanopore Technologies. Short- and long-reads were combined with Unicycler. Assemblies were investigated for multilocus sequence typing (MLST), antimicrobial resistance genes, porins, and plasmids. Results: The K. pneumoniae isolate (KP\_RM\_1) was resistant to CAZ-AVI, expanded-spectrum cephalosporins, amikacin, ertapenem, and cefiderocol (FDC) but was susceptible to tigecycline, colistin, trimethoprim/sulfamethoxazole, meropenem–vaborbactam, and imipenem–relebactam. WGS revealed that the KP\_RM\_1 genome is composed of a single chromosome of 5 Mbp and five circular plasmids. Further analysis showed the presence of novel blaKPC-216 located on a 72 kb plasmid. KPC-216 differs from KPC-3 by a Lysin (K) insertion at position 168 (+K168). Conclusions: We report the identification of a new KPC-3 variant associated with CAZ-AVI resistance. The KPC variants associated with CAZ-AVI resistance should be determined to promptly inform clinicians and start the appropriate antimicrobial therapy.},
+ author = {Giufrè, Maria and Errico, Giulia and Del Grosso, Maria and Pagnotta, Michela and Palazzotti, Bernardetta and Ballardini, Milva and Pantosti, Annalisa and Meledandri, Marcello and Monaco, Monica},
+ copyright = {http://creativecommons.org/licenses/by/3.0/},
+ doi = {10.3390/antibiotics13060507},
+ issn = {2079-6382},
+ journal = {Antibiotics},
+ keywords = {{\textgreater}UseGalaxy.eu, ESKAPE, KPC-216, cefiderocol, ceftazidime-avibactam, cross-resistance},
+ language = {en},
+ month = {June},
+ note = {Number: 6
+Publisher: Multidisciplinary Digital Publishing Institute},
+ number = {6},
+ pages = {507},
+ title = {Detection of {KPC}-216, a {Novel} {KPC}-3 {Variant}, in a {Clinical} {Isolate} of {Klebsiella} pneumoniae {ST101} {Co}-{Resistant} to {Ceftazidime}-{Avibactam} and {Cefiderocol}},
+ url = {https://www.mdpi.com/2079-6382/13/6/507},
+ urldate = {2024-06-07},
+ volume = {13},
+ year = {2024}
+}
+
 @article{gjaltema_distal_2021,
  author = {Gjaltema, Rutger A. F. and Schwämmle, Till and Kautz, Pauline and Robson, Michael and Schöpflin, Robert and Lustig, Liat Ravid and Brandenburg, Lennart and Dunkel, Ilona and Vechiatto, Carolina and Ntini, Evgenia and Mutzel, Verena and Schmiedel, Vera and Marsico, Annalisa and Mundlos, Stefan and Schulz, Edda G.},
  doi = {10.1101/2021.03.29.437476},
@@ -4918,6 +4984,23 @@ @article{jhinjharia_high-throughput_2023
  year = {2023}
 }
 
+@incollection{jia_salmonella_2024,
+ abstract = {Salmonella is a widespread pathogen that can cause a variety of disease syndromes, thereby having a tremendous impact on human health and animal husbandry. Currently, whole genome sequencing technology has been widely used to study the phylogenetic relationships of Salmonella, primarily using the Illumina short-read platform. Complete genome sequence data of Salmonella are rarely systematically analyzed in similar studies considering the relatively high cost currently. Therefore, here we collected the complete genome sequence data of 1819 Salmonella in GenBank and classified these strains into different subspecies, serovars, and STs by SISTR, Seqsero2, multilocus sequence typing (MLST), and other sophisticated software. In addition, we constructed and demonstrated different phylogenetic trees by four methods with high discriminatory power: core single-nucleotide polymorphism typing, core genome MLST (cgMLST), clustered regularly interspaced short palindromic repeat typing, and pan-genome typing. The different typing methods are systematically presented, along with a comparison of the characteristics of the four distinct typing methods used in this chapter. In conclusion, we have made a new attempt to use complete genome sequence datasets to study the phylogenetic relationships of Salmonella. Additional considerations regarding the time required to be consumed, the clustering effect, and the cgMLST method are also discussed.},
+ author = {Jia, Chenghao and Zhou, Haiyang and Wang, Zining and Liu, Yuhao and Yue, Min},
+ booktitle = {Phylogenomics},
+ doi = {10.1016/B978-0-323-99886-4.00019-3},
+ editor = {Mokrousov, Igor and Shitikov, Egor},
+ isbn = {978-0-323-99886-4},
+ keywords = {{\textgreater}UseGalaxy.eu, CRISPR typing, cgMLST, core SNP typing, pan-genome typing, phylogenomic analysis},
+ month = {January},
+ pages = {267--281},
+ publisher = {Academic Press},
+ title = {\textit{{Salmonella}} phylogenomics},
+ url = {https://www.sciencedirect.com/science/article/pii/B9780323998864000193},
+ urldate = {2024-06-07},
+ year = {2024}
+}
+
 @article{joshi_physicochemical_2024,
  abstract = {Prostate cancer is the most common cancer among men which has major diagnosis in the United States in 2017. Among DYRK class II members, dual specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2) is the functional target for prostate cancer treatment. Studies show that subfamilies of DYRKs are also capable to phosphorylate (tyrosine, serine, and threonine) residues, yet little research has been carried out for its inhibitors. In this article, conceptual density theory is used to estimate the physicochemical properties of 30 experimentally synthesized inhibitors targeting DYRK2. The HOMO–LUMO gap showed low reactivity and high chemical activity for the inhibitors. The biological efficacy of these 30 inhibitors is predicted by bioavailability, mutagenicity, and cardiotoxicity measures. The inhibitors showed low toxicity and no blood brain barrier permeability. Results indicated that the physiological actions of these inhibitors involve multiple target interactions. Since the experimental results of the DYRK2 protein showed great water solubility, favorable safety properties, and potential anti-prostate cancer activities for ligand 24, docking and molecular dynamics simulations from the Galaxy webserver using Gromacs open-source tools are also performed for (DYRK2-24) complex (PDB: 7EJV). (DYRK2-24) showed strong binding affinity and noncovalent interactions.},
  author = {Joshi, Sravani and Srivastava, Ruby},
@@ -4954,6 +5037,27 @@ @article{joshi_tracing_2024
  year = {2024}
 }
 
+@article{jovovic_novo_2024,
+ abstract = {Isopods are a diverse group of crustaceans, that inhabit various environments, including terrestrial, freshwater, and marine, both on the surface and in the underground. The biological mechanisms underlying their wide range of adaptations to diverse ecological niches remain elusive. In order to unravel the molecular basis of their adaptability, we generated a comprehensive RNAseq dataset comprising 11 isopod species belonging to the three different suborders: freshwater Asellota, marine, brackish and freshwater Sphaeromatidea, and terrestrial Oniscidea, with representatives from families Asellidae, Sphaeromatidae, and Trichoniscidae, respectively. Representatives of each family were collected from both cave and surface environments, representing at least three independent cave colonization events. Three biological replicates were sequenced from each species to ensure data robustness. The 11 high-quality RNAseq datasets will serve as a valuable resource for understanding cave-specific adaptations, comparative and functional genomics, ecological annotation as well as aid in conservation efforts of these non-model organisms. Importantly, transcriptomes of eight featured species have been made publicly accessible for the first time.},
+ author = {Jovović, Lada and Bedek, Jana and Malard, Florian and Bilandžija, Helena},
+ copyright = {2024 The Author(s)},
+ doi = {10.1038/s41597-024-03393-y},
+ issn = {2052-4463},
+ journal = {Scientific Data},
+ keywords = {{\textgreater}UseGalaxy.eu, Molecular ecology, Molecular evolution, Transcriptomics},
+ language = {en},
+ month = {June},
+ note = {Publisher: Nature Publishing Group},
+ number = {1},
+ pages = {595},
+ shorttitle = {De novo transcriptomes of cave and surface isopod crustaceans},
+ title = {De novo transcriptomes of cave and surface isopod crustaceans: insights from 11 species across three suborders},
+ url = {https://www.nature.com/articles/s41597-024-03393-y},
+ urldate = {2024-06-08},
+ volume = {11},
+ year = {2024}
+}
+
 @article{jude_draft_2019,
  abstract = {Chitinimonas spp. are Gram-negative bacilli that are observed in freshwater and soil sources. A number of Chitinimonas species have been characterized, including the green-pigmented Chitinimonas viridis. The isolate described here, BJB300, was obtained from a freshwater source in the Hudson Valley, NY. BJB300 is the first Chitinimonas isolate expressing violacein, a pigment with biotherapeutic potential.},
  author = {Jude, Brooke A.},
@@ -5079,6 +5183,27 @@ @article{kandinov_emergence_2023
  year = {2023}
 }
 
+@article{kandinov_mini-multilocus_2024,
+ abstract = {The increasing problem of antimicrobial resistance in N. gonorrhoeae necessitates the development of molecular typing schemes that are suitable for rapid and mass screening. The objective of this study was to design and validate a mini-MLST scheme for N. gonorrhoeae based on global pathogen population data. Using sequences of seven housekeeping genes of 21,402 isolates with known MLSTs from the PubMLST database, we identified eighteen informative polymorphisms and obtained mini-MLST nucleotide profiles to predict MLSTs of isolates. We proposed a new MLST grouping system for N. gonorrhoeae based on mini-MLST profiles. Phylogenetic analysis revealed that MLST genogroups are a stable characteristic of the N. gonorrhoeae global population. The proposed grouping system has been shown to bring together isolates with similar antimicrobial susceptibility, as demonstrated by the characteristics of major genogroups. Established MLST prediction algorithms based on nucleotide profiles are now publicly available. The mini-MLST scheme was evaluated using a MLST detection/prediction method based on the original hydrogel DNA microarray. The results confirmed a high predictive ability up to the MLST genogroup. The proposed holistic approach to gonococcal population analysis can be used for the continuous surveillance of known and emerging resistant N. gonorrhoeae isolates.},
+ author = {Kandinov, Ilya and Shaskolskiy, Boris and Kravtsov, Dmitry and Filippova, Marina and Larkin, Anatoliy and Gryadunov, Dmitry},
+ copyright = {http://creativecommons.org/licenses/by/3.0/},
+ doi = {10.3390/ijms25115781},
+ issn = {1422-0067},
+ journal = {International Journal of Molecular Sciences},
+ keywords = {\textit{Neisseria gonorrhoeae}, {\textgreater}UseGalaxy.eu, antimicrobial resistance, genogroups, informative polymorphisms, multilocus sequence typing, oligonucleotide microarray, phylogenetic analysis},
+ language = {en},
+ month = {January},
+ note = {Number: 11
+Publisher: Multidisciplinary Digital Publishing Institute},
+ number = {11},
+ pages = {5781},
+ title = {Mini-{Multilocus} {Sequence} {Typing} {Scheme} for the {Global} {Population} of {Neisseria} gonorrhoeae},
+ url = {https://www.mdpi.com/1422-0067/25/11/5781},
+ urldate = {2024-06-07},
+ volume = {25},
+ year = {2024}
+}
+
 @article{karthik_foremost_2023,
  abstract = {Several Pasteurella like organisms isolated from various avian species were recently reclassified into new genus based on whole genome sequence analysis. One such Pasteurella like organism, Bisgaard taxon 14 was classified as Spirabiliibacterium mucosae. In the present study, a Gram-negative organism was isolated from ailing pigeons with respiratory infection from a farm in Tamil Nadu, India and the organism was misidentified as Burkholderia mallei by Vitek 2 compact system based on biochemical characterization. Since, B. mallei is highly pathogenic and zoonotic, to further confirm, 16S rDNA sequencing and analysis was carried out which revealed that the strain belonged to Bisgaard taxon 14 (Spirabiliibacterium mucosae). To further confirm the findings, whole genome sequencing of the isolate was performed. Whole genome phylogeny and average nucleotide identity (ANI) analysis showed that the genome was closely matching with Spirabiliibacterium mucosae type strain 20,609 /3. Hence, the strain from pigeon was named as Spirabiliibacterium mucosae TN\_CUL\_2021 and the genome was submitted in NCBI SRA database. The genome of S. mucosase TN\_CUL\_2021 is only the second genome available worldwide in the NCBI database. Comparative genome analysis of 26 Pasteurellaceae family strains revealed 1101 genes specific for Spirabiliibacterium mucosae. Similarly, luxS virulence gene was found only in S. mucosae and Bisgaardia hudsonensis strains. Since there are only 2 genomes available in the NCBI genome database, further studies on isolation of S. mucosae needs to be carried out to identify its epidemiology and pathogenesis so as to develop better diagnostic assays and vaccines.},
  author = {Karthik, Kumaragurubaran and Anbazhagan, Subbaiyan and Ananda Chitra, Murugesan and Ramya, Rajendran and Sridhar, Ramaswamy and Dhinakar Raj, Gopal},
@@ -6166,6 +6291,24 @@ @article{lopez-santamarina_evaluation_2022
  year = {2022}
 }
 
+@article{lopez_epigenomic_2024,
+ abstract = {In plants, epigenetic stress memory has so far been found to be largely transient. Here, we wanted to assess the heritability of heat stress-induced epigenetic and transcriptomic changes following woodland strawberry (Fragaria vesca) reproduction. Strawberry is an ideal model to study epigenetic inheritance because it presents two modes of reproduction: sexual (self-pollinated plants) and asexual (clonally propagated plants named daughter plants). Taking advantage of this model, we investigated whether heat stress-induced DNA methylation changes can be transmitted via asexual reproduction.},
+ author = {López, María-Estefanía and Denoyes, Béatrice and Bucher, Etienne},
+ doi = {10.1186/s12870-024-05093-6},
+ issn = {1471-2229},
+ journal = {BMC Plant Biology},
+ keywords = {{\textgreater}UseGalaxy.eu, Asexual, Epigenetic, Fragaria, Memory, Plant, Reproduction, Stress},
+ language = {en},
+ month = {May},
+ number = {1},
+ pages = {405},
+ title = {Epigenomic and transcriptomic persistence of heat stress memory in strawberry ({Fragaria} vesca)},
+ url = {https://doi.org/10.1186/s12870-024-05093-6},
+ urldate = {2024-06-07},
+ volume = {24},
+ year = {2024}
+}
+
 @article{lother_diabetes_2020,
  abstract = {{\textless}h2{\textgreater}Abstract{\textless}/h2{\textgreater}{\textless}h3{\textgreater}Background{\textless}/h3{\textgreater}{\textless}p{\textgreater}Diabetes mellitus is a worldwide epidemic that causes high mortality due to cardiovascular complications, in particular heart failure. Diabetes is associated with profound pathophysiological changes in the heart. The aim of this study was to investigate the impact of diabetes on gene expression and DNA methylation in cardiac cells.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Methods and results{\textless}/h3{\textgreater}{\textless}p{\textgreater}Transcriptome analysis of heart tissue from mice with streptozotocin-induced diabetes revealed only 39 genes regulated, whereas cell type-specific analysis of the diabetic heart was more sensitive and more specific than heart tissue analysis and revealed a total of 3205 differentially regulated genes in five cell types. Whole genome DNA methylation analysis with basepair resolution of distinct cardiac cell types identified highly specific DNA methylation signatures of genic and regulatory regions. Interestingly, despite marked changes in gene expression, DNA methylation remained stable in streptozotocin-induced diabetes. Integrated analysis of cell type-specific gene expression enabled us to assign the particular contribution of single cell types to the pathophysiology of the diabetic heart. Finally, analysis of gene regulation revealed ligand-receptor pairs as potential mediators of heterocellular interaction in the diabetic heart, with fibroblasts and monocytes showing the highest degree of interaction.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusion{\textless}/h3{\textgreater}{\textless}p{\textgreater}In summary, cell type-specific analysis reveals differentially regulated gene programs that are associated with distinct biological processes in diabetes. Interestingly, despite these changes in gene expression, cell type-specific DNA methylation signatures of genic and regulatory regions remain stable in diabetes. Analysis of heterocellular interactions in the diabetic heart suggest that the interplay between fibroblasts and monocytes is of pivotal importance.{\textless}/p{\textgreater}},
  author = {Lother, Achim and Bondareva, Olga and Saadatmand, Ali R. and Pollmeier, Luisa and Härdtner, Carmen and Hilgendorf, Ingo and Weichenhan, Dieter and Eckstein, Volker and Plass, Christoph and Bode, Christoph and Backs, Johannes and Hein, Lutz and Gilsbach, Ralf},
@@ -6536,7 +6679,7 @@ @article{mcdonald_ultraviolet_2022
  year = {2022}
 }
 
-@article{mcdonald_ultraviolet_2022-1,
+@article{mcdonald_ultraviolet_2022,
  author = {McDonald, Marisa S. and Palecanda, Sitara and Cohen, Jonathan H. and Porter, Megan L.},
  doi = {10.1242/jeb.243256},
  journal = {Journal of Experimental Biology},
@@ -7341,6 +7484,15 @@ @article{noauthor_characterization_2023
  year = {2023}
 }
 
+@misc{noauthor_effect_2024,
+ keywords = {{\textgreater}UseGalaxy.eu},
+ month = {January},
+ title = {Effect of {Anti}‐{S100A4} {Monoclonal} {Antibody} {Treatment} on {Experimental} {Skin} {Fibrosis} and {Systemic} {Sclerosis}–{Specific} {Transcriptional} {Signatures} in {Human} {Skin} - {Trinh}‐{Minh} - 2024 - {Arthritis} \& {Rheumatology} - {Wiley} {Online} {Library}},
+ url = {https://acrjournals.onlinelibrary.wiley.com/doi/10.1002/art.42781},
+ urldate = {2024-06-07},
+ year = {2024}
+}
+
 @misc{noauthor_importance_2020,
  abstract = {Background: Current peak callers for identifying RNA-binding protein (RBP) binding sites from CLIP-seq data take into account genomic read profiles, but they ignore the underlying transcript information, that is information regarding splicing events. So far, there are no studies available that...},
  doi = {10.21203/rs.3.rs-18225/v1},
@@ -7353,6 +7505,15 @@ @misc{noauthor_importance_2020
  year = {2020}
 }
 
+@misc{noauthor_nutrients_2024,
+ keywords = {{\textgreater}UseGalaxy.eu},
+ month = {January},
+ title = {Nutrients {\textbar} {Free} {Full}-{Text} {\textbar} {A} 14-{Day} {Double}-{Blind}, {Randomized}, {Controlled} {Crossover} {Intervention} {Study} with {Anti}-{Bacterial} {Benzyl} {Isothiocyanate} from {Nasturtium} ({Tropaeolum} majus) on {Human} {Gut} {Microbiome} and {Host} {Defense}},
+ url = {https://www.mdpi.com/2072-6643/16/3/373},
+ urldate = {2024-06-07},
+ year = {2024}
+}
+
 @article{noauthor_proceedings_2023,
  keywords = {{\textgreater}UseGalaxy.eu},
  title = {Proceedings of the {Joint} 3rd {International} {Conference} on {Bioinformatics} and {Data} {Science} ({ICBDS} 2022), {ISBN} 9789464631630 - {Better} {Read} {Than} {Dead} {Bookstore} {Newtown}},
@@ -7627,6 +7788,23 @@ @article{owen_rna-sequencing_2019
  year = {2019}
 }
 
+@article{pachanon_genomic_2024,
+ abstract = {Carbapenem and colistin-resistant Enterobacteriaceae, including Klebsiella pneumoniae, have become a growing global concern, posing a significant threat to public health. Currently, there is limited information about the genetic background of carbapenem and colistin-resistant K. pneumoniae isolates infecting humans and dogs in Thailand. This study aimed to characterize carbapenem and colistin-resistant genes in six resistant K. pneumoniae clinical isolates (three from humans and three from dogs) which differed in their pulse field gel electrophoresis profiles. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), antimicrobial susceptibility testing, and whole-genome sequencing were employed to identify and analyze the isolates. All six isolates were carbapenemase-producing K. pneumoniae isolates with chromosomally carried blaSHV, fosA, oqxA and oqxB genes, as well as nine to 21 virulence genes. The isolates belonged to five multilocus sequence types (STs): one isolate from a human and one from a dog belonged to ST16, with the other two human isolates being from ST340 and ST1269 and the other two dog isolates were ST147 and ST15. One human isolate and two dog isolates harbored the same blaOXA-232 gene on the ColKP3 plasmid, and one dog isolate carried the blaOXA-48 gene on the IncFII plasmid. Notably, one human isolate exhibited resistance to colistin mediated by the mcr-3.5 gene carried on the IncFII plasmid, which co-existed with resistance determinants to other antibiotics, including aminoglycosides and quinolones. In conclusion, this study provides a comprehensive characterization of both chromosome- and plasmid-mediated carbapenem and colistin resistance in a set of K. pneumoniae clinical isolates from unrelated humans and dogs in Thailand. The similarities and differences found contribute to our understanding of the potential widescale dissemination of these important resistance genes among clinical isolates from humans and animals, which in turn may contribute to outbreaks of emerging resistant clones in hospital settings.},
+ author = {Pachanon, Ruttana and Khine, Nwai Oo and Phumthanakorn, Nathita and Wongsurawat, Thidathip and Niyomtham, Waree and Chatsuwan, Tanittha and Hampson, David J. and Prapasarakul, Nuvee},
+ doi = {10.3389/fvets.2024.1386496},
+ issn = {2297-1769},
+ journal = {Frontiers in Veterinary Science},
+ keywords = {{\textgreater}UseGalaxy.eu, Carbapenem resistance, Colistin resistance, Klebsiella pneumoniae, Plasmidmediated resistance, whole genome analysis},
+ language = {English},
+ month = {May},
+ note = {Publisher: Frontiers},
+ title = {Genomic characterization of carbapenem and colistin-resistant {Klebsiella} pneumoniae isolates from humans and dogs},
+ url = {https://www.frontiersin.org/articles/10.3389/fvets.2024.1386496},
+ urldate = {2024-06-07},
+ volume = {11},
+ year = {2024}
+}
+
 @article{page-karjian_fibropapillomatosis_2021,
  author = {Page-Karjian, Annie and Whitmore, Liam and Stacy, Brian A. and Perrault, Justin R. and Farrell, Jessica A. and Shaver, Donna J. and Walker, J. Shelby and Frandsen, Hilary R. and Rantonen, Elina and Harms, Craig A. and Norton, Terry M. and Innis, Charles and Yetsko, Kelsey and Duffy, David J.},
  doi = {10.3390/ani11113076},
@@ -7794,6 +7972,21 @@ @article{patel_bioprospecting_2023
  year = {2023}
 }
 
+@article{pazoki_elucidating_2024,
+ abstract = {Genetic abnormalities like Y chromosome microdeletions are implicated in male infertility. This study investigated the association of azoospermia factor (AZF) region microdeletions with unsuccessful assisted reproductive techniques (ART), including in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI).This cross-sectional analysis study examined 80 Iranian oligospermic men (mean age 34 years) with prior failed ICSI and IVF cycles (IR.IAU.TNB.REC.1401.041). Semen analysis evaluated quantity/quality parameters based on World Health Organization guidelines. Participants were stratified by sperm DNA fragmentation (SDF) levels into: control (SDF \< 15\%, n = 20), mild elevation (15\% ≤ SDF ≤ 30\%, n = 60), and high (SDF \> 30\%, n = 20). Multiplex PCR mapped AZF microdeletions in the high SDF group. The AZF-associated genes were selected by RNA Seq analysis, and the candidate genes were checked for expression level by real-time PCR.High SDF individuals exhibited poorer semen metrics, including 69\% lower sperm concentration (P = 0.04) than those without SDF. Of this subset, 45\% (9/20 men) harboured predominately AZF microdeletions. Men with AZF microdeletions showed higher SDF (32\% vs 21\%, P = 0.02) and altered AZF-associated genes expression. As USP9Y 3-fold, UTY 1.3-fold, and BPY2 1-fold revealed up-regulation, while IQCF1 8-fold, CDY 6.5-fold, DAZ 6-fold, and DDX3Y 1-fold underwent down-regulation. The PAWP gene was also down-regulated (5.7-fold, P = 0.029) in the IVF/ICSI failure group.AZF microdeletions significantly impact male infertility and ART outcomes. High SDF individuals exhibited poorer semen metrics, with 45\% AZF microdeletions. These microdeletions altered AZF-associated genes expression, affecting fertility mediator PAWP independently. Dual AZF and SDF screening enables personalized management in severe male infertility, potentially explaining IVF/ICSI failures.},
+ author = {Pazoki, Nasrin and Salehi, Mitra and Angaji, Seyed Abdolhamid and Abdollahpour-Alitappeh, Meghdad},
+ doi = {10.1093/hmg/ddae086},
+ issn = {0964-6906},
+ journal = {Human Molecular Genetics},
+ keywords = {{\textgreater}UseGalaxy.eu},
+ month = {May},
+ pages = {ddae086},
+ title = {Elucidating the impact of {Y} chromosome microdeletions and altered gene expression on male fertility in assisted reproduction},
+ url = {https://doi.org/10.1093/hmg/ddae086},
+ urldate = {2024-06-07},
+ year = {2024}
+}
+
 @article{pelletier_standardized_2021,
  author = {Pelletier, Dominique and Roos, David and Bouchoucha, Marc and Schohn, Thomas and Roman, William and Gonson, Charles and Bockel, Thomas and Carpentier, Liliane and Preuss, Bastien and Powell, Abigail and Garcia, Jessica and Gaboriau, Matthias and Cadé, Florent and Royaux, Coline and Bras, Yvan Le and Reecht, Yves},
  doi = {10.3389/fmars.2021.689280},
@@ -8127,6 +8320,27 @@ @article{pinto_rescue_2024
  year = {2024}
 }
 
+@article{pirnay_personalized_2024,
+ abstract = {In contrast to the many reports of successful real-world cases of personalized bacteriophage therapy (BT), randomized controlled trials of non-personalized bacteriophage products have not produced the expected results. Here we present the outcomes of a retrospective observational analysis of the first 100 consecutive cases of personalized BT of difficult-to-treat infections facilitated by a Belgian consortium in 35 hospitals, 29 cities and 12 countries during the period from 1 January 2008 to 30 April 2022. We assessed how often personalized BT produced a positive clinical outcome (general efficacy) and performed a regression analysis to identify functional relationships. The most common indications were lower respiratory tract, skin and soft tissue, and bone infections, and involved combinations of 26 bacteriophages and 6 defined bacteriophage cocktails, individually selected and sometimes pre-adapted to target the causative bacterial pathogens. Clinical improvement and eradication of the targeted bacteria were reported for 77.2\% and 61.3\% of infections, respectively. In our dataset of 100 cases, eradication was 70\% less probable when no concomitant antibiotics were used (odds ratio = 0.3; 95\% confidence interval = 0.127–0.749). In vivo selection of bacteriophage resistance and in vitro bacteriophage–antibiotic synergy were documented in 43.8\% (7/16 patients) and 90\% (9/10) of evaluated patients, respectively. We observed a combination of antibiotic re-sensitization and reduced virulence in bacteriophage-resistant bacterial isolates that emerged during BT. Bacteriophage immune neutralization was observed in 38.5\% (5/13) of screened patients. Fifteen adverse events were reported, including seven non-serious adverse drug reactions suspected to be linked to BT. While our analysis is limited by the uncontrolled nature of these data, it indicates that BT can be effective in combination with antibiotics and can inform the design of future controlled clinical trials. BT100 study, ClinicalTrials.gov registration: NCT05498363.},
+ author = {Pirnay, Jean-Paul and Djebara, Sarah and Steurs, Griet and Griselain, Johann and Cochez, Christel and De Soir, Steven and Glonti, Tea and Spiessens, An and Vanden Berghe, Emily and Green, Sabrina and Wagemans, Jeroen and Lood, Cédric and Schrevens, Eddie and Chanishvili, Nina and Kutateladze, Mzia and de Jode, Mathieu and Ceyssens, Pieter-Jan and Draye, Jean-Pierre and Verbeken, Gilbert and De Vos, Daniel and Rose, Thomas and Onsea, Jolien and Van Nieuwenhuyse, Brieuc and Soentjens, Patrick and Lavigne, Rob and Merabishvili, Maya},
+ copyright = {2024 The Author(s)},
+ doi = {10.1038/s41564-024-01705-x},
+ issn = {2058-5276},
+ journal = {Nature Microbiology},
+ keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance, Bacterial genetics, Bacterial infection, Bacteriophages},
+ language = {en},
+ month = {June},
+ note = {Publisher: Nature Publishing Group},
+ number = {6},
+ pages = {1434--1453},
+ shorttitle = {Personalized bacteriophage therapy outcomes for 100 consecutive cases},
+ title = {Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study},
+ url = {https://www.nature.com/articles/s41564-024-01705-x},
+ urldate = {2024-06-07},
+ volume = {9},
+ year = {2024}
+}
+
 @article{plaza_genomic_2023,
  author = {Plaza, David Fernando and Zerebinski, Julia and Broumou, Ioanna and Lautenbach, Maximilian Julius and Ngasala, Billy and Sundling, Christopher and Färnert, Anna},
  doi = {10.1016/j.crmeth.2023.100574},
@@ -8327,6 +8541,21 @@ @article{rajczewski_rigorous_2021
  year = {2021}
 }
 
+@article{ramos_mobilome_2024,
+ abstract = {Staphylococcus aureus thrives at animal-human-environment interfaces. A large-scale work from our group indicated that antimicrobial resistance (AMR) in commensal S. aureus strains from wild ungulates is associated with agricultural land cover and livestock farming, raising the hypothesis that AMR genes in wildlife strains may originate from different hosts, namely via exchange of mobile genetic elements (MGE). In this work, we generate the largest available dataset of S. aureus draft genomes from wild ungulates in Portugal and explore their mobilome, which can determine important traits such as AMR, virulence, and host specificity, to understand MGE exchange. Core genome multi-locus sequence typing based on 98 newly generated draft genomes and 101 publicly available genomes from Portugal demonstrated that the genomic relatedness of S. aureus from wild ungulates assigned to livestock-associated sequence types (ST) is greater compared to wild ungulate isolates assigned to human-associated STs. Screening of host specificity determinants disclosed the unexpected presence in wildlife of the immune evasion cluster encoded in φSa3 prophage, described as a human-specific virulence determinant. Additionally, two plasmids, pAVX and pETB, previously associated with avian species and humans, respectively, and the Tn553 transposon were detected. Both pETB and Tn553 encode penicillin resistance through blaZ. Pangenome analysis of wild ungulate isolates shows a core genome fraction of 2133 genes, with isolates assigned to ST72 and ST3224 being distinguished from the remaining by MGEs, although there is no reported role of these in adaptation to wildlife. AMR related gene clusters found in the shell genome are directly linked to resistance against penicillin, macrolides, fosfomycin, and aminoglycosides, and they represent mobile ARGs. Altogether, our findings support epidemiological interactions of human and non-human hosts at interfaces, with MGE exchange, including AMR determinants, associated with putative indirect movements of S. aureus among human and wildlife hosts that might be bridged by livestock.},
+ author = {Ramos, Beatriz and Cunha, Mónica V.},
+ doi = {10.1016/j.envpol.2024.124241},
+ issn = {0269-7491},
+ journal = {Environmental Pollution},
+ keywords = {{\textgreater}UseGalaxy.eu, antimicrobial resistance, cgMLST, mobile genetic element, wildlife},
+ month = {May},
+ pages = {124241},
+ title = {The mobilome of \textit{{Staphylococcus} aureus} from wild ungulates reveals epidemiological links at the animal-human interface},
+ url = {https://www.sciencedirect.com/science/article/pii/S0269749124009552},
+ urldate = {2024-06-04},
+ year = {2024}
+}
+
 @article{ranchou-peyruse_microbial_2021,
  author = {Ranchou-Peyruse, Magali and Guignard, Marion and Casteran, Franck and Abadie, Maïder and Defois, Clémence and Peyret, Pierre and Dequidt, David and Caumette, Guilhem and Chiquet, Pierre and Cézac, Pierre and Ranchou-Peyruse, Anthony},
  doi = {10.3389/fmicb.2021.688929},
@@ -8648,6 +8877,24 @@ @article{roux_dna_2023
  year = {2023}
 }
 
+@article{royaux_genetic_2024,
+ abstract = {Thirteen new freshwater populations of the copepod genus BoeckellaDe Guerne \& Richard, 1889 were found during three expeditions to New Caledonia (‘La Planète Revisitée,’ 2016-2018). The 12 populations from the Plaine des Lacs, which show remarkable genetic diversity among themselves, were identified as B. spinogibbaDefaye, 1998, the only species of its genus known from New Caledonia until now. The sole exception, the population from Mont-Dore 22 km further east, appeared genetically and morphologically distinct from the others and is described herein as a new species. The two species are distinguished from each other by the shapes of the male and female P5, female Th5, and body colour. A previously published key is amended to separate the species. Our concatenated COI+28S phylogeny places the two New Caledonia species as a new branch within Boeckella, distinct from the branches consisting of South American, Antarctic and Australasian species. All 13 Boeckella populations inhabit the extreme south of New Caledonia, an area known for endemism and high heavy metal concentrations in the soil. Extensive mining activity in this metal-rich area, begun in 1873, is now leading to conflict with conservation goals. By using aerial photographs to trace the fate of the pond that is the type locality of B. spinogibba, we confirmed that it disappeared between 2007 and 2014 as a result of the expansion of the Goro nickel mine.},
+ author = {Royaux, Coline and Charpin, Nicolas and Rabet, Nicolas},
+ doi = {10.1093/jcbiol/ruae001},
+ issn = {0278-0372},
+ journal = {Journal of Crustacean Biology},
+ keywords = {{\textgreater}UseGalaxy.eu},
+ month = {March},
+ number = {1},
+ pages = {ruae001},
+ shorttitle = {Genetic variability of {New} {Caledonian} {Boeckella} {De} {Guerne} \& {Richard}, 1889 ({Copepoda}},
+ title = {Genetic variability of {New} {Caledonian} {Boeckella} {De} {Guerne} \& {Richard}, 1889 ({Copepoda}: {Calanoida}), with the description of a new species},
+ url = {https://doi.org/10.1093/jcbiol/ruae001},
+ urldate = {2024-06-07},
+ volume = {44},
+ year = {2024}
+}
+
 @article{royaux_genetic_2024,
  abstract = {Thirteen new freshwater populations of the copepod genus BoeckellaDe Guerne \& Richard, 1889 were found during three expeditions to New Caledonia (‘La Planète Revisitée,’ 2016-2018). The 12 populations from the Plaine des Lacs, which show remarkable genetic diversity among themselves, were identified as B. spinogibbaDefaye, 1998, the only species of its genus known from New Caledonia until now. The sole exception, the population from Mont-Dore 22 km further east, appeared genetically and morphologically distinct from the others and is described herein as a new species. The two species are distinguished from each other by the shapes of the male and female P5, female Th5, and body colour. A previously published key is amended to separate the species. Our concatenated COI+28S phylogeny places the two New Caledonia species as a new branch within Boeckella, distinct from the branches consisting of South American, Antarctic and Australasian species. All 13 Boeckella populations inhabit the extreme south of New Caledonia, an area known for endemism and high heavy metal concentrations in the soil. Extensive mining activity in this metal-rich area, begun in 1873, is now leading to conflict with conservation goals. By using aerial photographs to trace the fate of the pond that is the type locality of B. spinogibba, we confirmed that it disappeared between 2007 and 2014 as a result of the expansion of the Goro nickel mine.},
  author = {Royaux, Coline and Charpin, Nicolas and Rabet, Nicolas},
@@ -8966,6 +9213,24 @@ @article{schlecht_transcriptomic_2020
  year = {2020}
 }
 
+@article{schmidt_practical_2024,
+ abstract = {Bioimage data are generated in diverse research fields throughout the life and biomedical sciences. Its potential for advancing scientific progress via modern, data-driven discovery approaches reaches beyond disciplinary borders. To fully exploit this potential, it is necessary to make bioimaging data, in general, multidimensional microscopy images and image series, FAIR, that is, findable, accessible, interoperable and reusable. These FAIR principles for research data management are now widely accepted in the scientific community and have been adopted by funding agencies, policymakers and publishers. To remain competitive and at the forefront of research, implementing the FAIR principles into daily routines is an essential but challenging task for researchers and research infrastructures. Imaging core facilities, well-established providers of access to imaging equipment and expertise, are in an excellent position to lead this transformation in bioimaging research data management. They are positioned at the intersection of research groups, IT infrastructure providers, the institution´s administration, and microscope vendors. In the frame of German BioImaging – Society for Microscopy and Image Analysis (GerBI-GMB), cross-institutional working groups and third-party funded projects were initiated in recent years to advance the bioimaging community's capability and capacity for FAIR bioimage data management. Here, we provide an imaging-core-facility-centric perspective outlining the experience and current strategies in Germany to facilitate the practical adoption of the FAIR principles closely aligned with the international bioimaging community. We highlight which tools and services are ready to be implemented and what the future directions for FAIR bioimage data have to offer.},
+ author = {Schmidt, Christian and Boissonnet, Tom and Dohle, Julia and Bernhardt, Karen and Ferrando-May, Elisa and Wernet, Tobias and Nitschke, Roland and Kunis, Susanne and Weidtkamp-Peters, Stefanie},
+ doi = {10.1111/jmi.13317},
+ issn = {1365-2818},
+ journal = {Journal of Microscopy},
+ keywords = {{\textgreater}UseGalaxy.eu, FAIR, OMERO, bioimaging, data stewardship, research data management},
+ language = {en},
+ note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jmi.13317},
+ number = {3},
+ pages = {350--371},
+ title = {A practical guide to bioimaging research data management in core facilities},
+ url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jmi.13317},
+ urldate = {2024-06-07},
+ volume = {294},
+ year = {2024}
+}
+
 @article{schoof_mouse_2023,
  abstract = {Pediatric high-grade gliomas of the subclass MYCN (HGG-MYCN) are highly aggressive tumors frequently carrying MYCN amplifications, TP53 mutations, or both alterations. Due to their rarity, such tumors have only recently been identified as a distinct entity, and biological as well as clinical characteristics have not been addressed specifically. To gain insights into tumorigenesis and molecular profiles of these tumors, and to ultimately suggest alternative treatment options, we generated a genetically engineered mouse model by breeding hGFAP-cre::Trp53Fl/Fl::lsl-MYCN mice. All mice developed aggressive forebrain tumors early in their lifetime that mimic human HGG-MYCN regarding histology, DNA methylation, and gene expression. Single-cell RNA sequencing revealed a high intratumoral heterogeneity with neuronal and oligodendroglial lineage signatures. High-throughput drug screening using both mouse and human tumor cells finally indicated high efficacy of Doxorubicin, Irinotecan, and Etoposide as possible therapy options that children with HGG-MYCN might benefit from.},
  author = {Schoof, Melanie and Godbole, Shweta and Albert, Thomas K. and Dottermusch, Matthias and Walter, Carolin and Ballast, Annika and Qin, Nan and Olivera, Marlena Baca and Göbel, Carolin and Neyazi, Sina and Holdhof, Dörthe and Kresbach, Catena and Peter, Levke-Sophie and Epplen, Gefion Dorothea and Thaden, Vanessa and Spohn, Michael and Blattner-Johnson, Mirjam and Modemann, Franziska and Mynarek, Martin and Rutkowski, Stefan and Sill, Martin and Varghese, Julian and Afflerbach, Ann-Kristin and Eckhardt, Alicia and Münter, Daniel and Verma, Archana and Struve, Nina and Jones, David T. W. and Remke, Marc and Neumann, Julia E. and Kerl, Kornelius and Schüller, Ulrich},
@@ -9353,6 +9618,43 @@ @article{soares_hierarchical_2021
  year = {2021}
 }
 
+@article{soggia_bioelectrochemical_2024,
+ abstract = {Microbial electrosynthesis (MES) cell use is an innovative approach for single-cell proteins (SCP) production. Coupling MES with the valorization of CO2 from anaerobic digestion and nitrogen from livestock effluents has beneficial environmental effects, reducing greenhouse gas emissions and nitrogen overloading. In addition, the reducing power needed can come from surplus renewable energy. In this study, MES with a biochar-functionalized cathode was tested at varying polarizations, i.e. non polarized, -0.6 V and -1.0 V vs Ag/AgCl, and biogas-derived CO2 and recovered ammonia from pig slurry was supplied. Negative polarization switched the microbial community from heterotrophic, typical of unpolarized MES, to a mix of both heterotrophic and autotrophic/electrotrophic communities at -0.6 V and to mainly autotrophic/electrotrophic at -1.0 V. The more negative polarization allowed the highest CO2 and N capture, i.e. 39 ± 2 \% of the supplied CO2, and 6.7 ± 0.8 \% supplied N. Microbial biomass characterization indicated a protein content on dry matter basis of 33.1 ± 1.3 \% (unpolarized), 43.2 ± 0.6 \% (-0.6 V) and 69.1 ± 1.0 \% (-1.0 V). The amino acids profiles investigated showed a high nutritional value of the produced biomass, not far from those of conventional protein sources used for producing feed/food.},
+ author = {Soggia, Gabriele and Goglio, Andrea and Cristiani, Pierangela and Luciani, Ivan and Clagnan, Elisa and Adani, Fabrizio},
+ doi = {10.1016/j.renene.2024.120761},
+ issn = {0960-1481},
+ journal = {Renewable Energy},
+ keywords = {{\textgreater}UseGalaxy.eu, Ammonia, Biocathode, Carbon dioxide, Microbial electrosynthesis, Power-to-protein, Single-cell protein},
+ month = {June},
+ pages = {120761},
+ title = {Bioelectrochemical protein production valorizing {NH3}-rich pig manure-derived wastewater and {CO2} from anaerobic digestion},
+ url = {https://www.sciencedirect.com/science/article/pii/S0960148124008292},
+ urldate = {2024-06-07},
+ year = {2024}
+}
+
+@article{soleau_first_2024,
+ abstract = {The emerging heteropathotype shigatoxigenic (STEC) and extra-intestinal pathogenic Escherichia coli (ExPEC) O80:H2 has been the second leading cause of pediatric HUS in France since the mid-2010s. In contrast with other highly pathogenic STEC serotypes, for which ruminants have clearly been identified as the main human infection source, this heteropathotype’s reservoir remains unknown. In this context, we describe for the first time the isolation of seven STEC O80:H2 strains from healthy cattle on a single cattle farm in France. This study aimed at (i) characterizing the genome and (ii) investigating the phylogenetic positions of these O80:H2 STEC strains. The virulomes, resistomes, and phylogenetic positions of the seven bovine isolates were investigated using in silico typing tools, antimicrobial susceptibility testing and cgMLST analysis after short-read whole genome sequencing (WGS). One representative isolate (A13P112V1) was also subjected to long-read sequencing. The seven isolates possessed ExPEC-related virulence genes on a pR444\_A-like mosaic plasmid, previously described in strain RDEx444 and known to confer multi-drug resistance. All isolates were clonally related and clustered with human clinical strains from France and Switzerland with a range of locus differences of only one to five. In conclusion, our findings suggest that healthy cattle in France could potentially act as a reservoir of the STEC-ExPEC O80:H2 pathotype.},
+ author = {Soleau, Nathan and Ganet, Sarah and Werlen, Stéphanie and Collignon, Lia and Cointe, Aurélie and Bonacorsi, Stéphane and Sergentet, Delphine},
+ copyright = {http://creativecommons.org/licenses/by/3.0/},
+ doi = {10.3390/ijms25105428},
+ issn = {1422-0067},
+ journal = {International Journal of Molecular Sciences},
+ keywords = {{\textgreater}UseGalaxy.eu, Shiga-toxin-producing \textit{Escherichia coli} (STEC), characterization, emerging pathogen, first isolation, serotype O80:H2, whole-genome sequencing},
+ language = {en},
+ month = {January},
+ note = {Number: 10
+Publisher: Multidisciplinary Digital Publishing Institute},
+ number = {10},
+ pages = {5428},
+ shorttitle = {First {Isolation} of the {Heteropathotype} {Shiga} {Toxin}-{Producing} and {Extra}-{Intestinal} {Pathogenic} ({STEC}-{ExPEC}) {E}. coli {O80}},
+ title = {First {Isolation} of the {Heteropathotype} {Shiga} {Toxin}-{Producing} and {Extra}-{Intestinal} {Pathogenic} ({STEC}-{ExPEC}) {E}. coli {O80}:{H2} in {French} {Healthy} {Cattle}: {Genomic} {Characterization} and {Phylogenetic} {Position}},
+ url = {https://www.mdpi.com/1422-0067/25/10/5428},
+ urldate = {2024-06-07},
+ volume = {25},
+ year = {2024}
+}
+
 @book{somashekhar_proceedings_2023,
  abstract = {This is an open access book. We are pleased to announce our 3rd International Conference on Bioinformatics and Data Science (ICBDS – 2022) and 9th International Conference on Public Mental Health and Neurosciences (ICPMN – 2022) which was a unique conference where we connectted Biological Function through Computational Genomics to the world of integrated medicine and therapeutics. Functional genomics is a field of molecular biology that attempts to describe gene (and protein) functions and interactions. This science aims to understand the complex relationship between genotype and phenotype on a global (genome-wide) scale of different biological processes. Most researchers now study genes or regions on a “genome-wide” scale (i.e. all or multiple genes/regions at the same time), with the hope of narrowing them down to a list of candidate genes or regions to analyze in more detail. There are several specific functional genomics approaches depending on what we are focused on DNA level (genomics and epigenomics), RNA level (transcriptomics), protein level (proteomics), metabolite level (metabolomics) and phenotype level (phenomics). The recent trends in gene and genome editing technologies, promising genomic information can be modulated in the areas of medicine, agriculture and environment. Big data is a promising in many research areas, but still it is computationally challenging and non-availability of experts to handle big-data with reduced speed and cost. With the increasing use of advanced technology and the exploding amount of big-data in, it is imperative to introduce effective and efficient methods to handle big data using computing technologies. The big data analytics technique is required to solve the problems in bioinformatics such as the storage of vast information generated by analyzing the big-data. Big data analytics can examine large data sets, analyze and correlate genomic and proteomic information. Big data research finds a huge application in Neuroscience and Brain research. Our unique conference connects genomics to the world of genomics to integrated medicine including yogic sciences.},
  author = {Somashekhar, R. and Bagchi, Preenon and Rajesh, T. S. and Hill, Richard and Rossi, Kathryn},
@@ -9945,6 +10247,27 @@ @article{tosar_ri-sec-seq_2021
  year = {2021}
 }
 
+@article{toth_divergence_2024,
+ abstract = {Phytoplasmas are linked to diseases in hundreds of economically important crops, including carrots. In carrots, phytoplasmosis is associated with leaf chlorosis and necrosis, coupled with inhibited root system development, ultimately leading to significant economic losses. During a field study conducted in Baden-Württemberg (Germany), two strains of the provisional taxon ‘Candidatus Phytoplasma asteris’ were identified within a carrot plot. For further analysis, strains M8 and M33 underwent shotgun sequencing, utilising single-molecule-real-time (SMRT) long-read sequencing and sequencing-by-synthesis (SBS) paired-end short-read sequencing techniques. Hybrid assemblies resulted in complete de novo assemblies of two genomes harboring circular chromosomes and two plasmids. Analyses, including average nucleotide identity and sequence comparisons of established marker genes, confirmed the phylogenetic divergence of ‘Ca. P. asteris’ and a different assignment of strains to the 16S rRNA subgroup I-A for M33 and I-B for M8. These groups exhibited unique features, encompassing virulence factors and genes, associated with the mobilome. In contrast, pan-genome analysis revealed a highly conserved gene set related to metabolism across these strains. This analysis of the Aster Yellows (AY) group reaffirms the perception of phytoplasmas as bacteria that have undergone extensive genome reduction during their co-evolution with the host and an increase of genome size by mobilome.},
+ author = {Toth, Rafael and Ilic, Anna-Marie and Huettel, Bruno and Duduk, Bojan and Kube, Michael},
+ copyright = {http://creativecommons.org/licenses/by/3.0/},
+ doi = {10.3390/microorganisms12051016},
+ issn = {2076-2607},
+ journal = {Microorganisms},
+ keywords = {{\textgreater}UseGalaxy.eu, carrot, hybrid assembly, phylogeny, virulence factors},
+ language = {en},
+ month = {May},
+ note = {Number: 5
+Publisher: Multidisciplinary Digital Publishing Institute},
+ number = {5},
+ pages = {1016},
+ title = {Divergence within the {Taxon} ‘{Candidatus} {Phytoplasma} asteris’ {Confirmed} by {Comparative} {Genome} {Analysis} of {Carrot} {Strains}},
+ url = {https://www.mdpi.com/2076-2607/12/5/1016},
+ urldate = {2024-06-07},
+ volume = {12},
+ year = {2024}
+}
+
 @article{toth_genomic_2024,
  abstract = {Extended-spectrum β-lactamase-producing Escherichia coli ST131 has become widespread worldwide. This study aims to characterize the virulome, resistome, and population structure of E. coli ST131 isolates from clinical blood samples in Hungary. A total of 30 C2/H30Rx and 33 C1-M27 ST131 isolates were selected for Illumina MiSeq sequencing and 30 isolates for MinION sequencing, followed by hybrid de novo assembly. Five C2/H30Rx and one C1-M27 cluster were identified. C1-M27 isolates harbored the F1:A2:B20 plasmid in 93.9\% of cases. Long-read sequencing revealed that blaCTX-M-27 was on plasmids. Among the C2/H30Rx isolates, only six isolates carried the C2-associated F2:A1:B- plasmid type. Of 19 hybrid-assembled C2/H30Rx genomes, the blaCTX-M-15 gene was located on plasmid only in one isolate, while in the other isolates, ISEcp1 or IS26-mediated chromosomal integration of blaCTX-M-15 was detected in unique variations. In one isolate a part of F2:A1:B- plasmid integrated into the chromosome. These results suggest that CTX-M-15-producing C2/H30Rx and CTX-M-27-producing C1-M27 subclades may have emerged and spread in different ways in Hungary. While blaCTX-M-27 was carried mainly on the C1/H30R-associated F1:A2:B20 plasmid, the IncF-like plasmids of C2/H30Rx or its composite transposons have been incorporated into the chromosome through convergent evolutionary processes.},
  author = {Tóth, Kinga and Damjanova, Ivelina and Laczkó, Levente and Buzgó, Lilla and Lesinszki, Virág and Ungvári, Erika and Jánvári, Laura and Hanczvikkel, Adrienn and Tóth, Ákos and Szabó, Dóra},
@@ -10347,6 +10670,22 @@ @article{voelker_terpene_2023
  year = {2023}
 }
 
+@article{volkova_multi-omics_2024,
+ abstract = {Barley is a resilient crop with high nutritional value and adaptability, making it a promising candidate for phytoremediation and space agriculture. The study presents a comprehensive multi-omics analysis of the impact of ionising radiation (IR) on barley seedlings, intending to identify candidate pathways for creating radiation-resilient barley plants. We found that different IR treatments (gamma, electron, proton, neutron) increased the intensity of protein catabolism and led to the attenuation of translation. The impact of IRs on protein synthesis and degradation was accompanied by rearrangements in energy metabolism and reallocation of nitrogen, probably due to enhanced protein catabolism. At least partially, those changes seem to fuel secondary metabolites production, including riboflavin, various phytoalexins, phytosiderophores, ferulic and sinapic acids, kaempferol, quercetin, nictoflorin, gallate, and podophyllotoxin. Many of these compounds have antioxidant or radioprotective properties. To focus on possible targets for gene editing, we identified genes differentially regulated after all types of IR exposure and potential transcription factors regulating secondary metabolism, including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC families.},
+ author = {Volkova, Polina and Prazyan, Alexandr and Podlutskii, Mikhail and Saburov, Vyacheslav and Kazakova, Elizaveta and Bitarishvili, Sofia and Duarte, Gustavo T. and Shesterikova, Ekaterina and Makarenko, Ekaterina and Lychenkova, Maria and Ben, Cécile and Gentzbittel, Laurent and Kazakov, Evgenii and Moiseev, Alexandr and Diuzhenko, Sergei and Korol, Marina and Bondarenko, Ekaterina},
+ doi = {10.1016/j.envexpbot.2023.105600},
+ issn = {0098-8472},
+ journal = {Environmental and Experimental Botany},
+ keywords = {{\textgreater}UseGalaxy.eu, Barley, Ionising radiation, Metabolomics, Multi-omics, Phytoremediation, Proteomics, Radioresistance, Secondary metabolites, Transcriptomics, Translation},
+ month = {February},
+ pages = {105600},
+ title = {Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation},
+ url = {https://www.sciencedirect.com/science/article/pii/S0098847223003957},
+ urldate = {2024-06-07},
+ volume = {218},
+ year = {2024}
+}
+
 @article{volkova_multi-omics_2024,
  abstract = {Barley is a resilient crop with high nutritional value and adaptability, making it a promising candidate for phytoremediation and space agriculture. The study presents a comprehensive multi-omics analysis of the impact of ionising radiation (IR) on barley seedlings, intending to identify candidate pathways for creating radiation-resilient barley plants. We found that different IR treatments (gamma, electron, proton, neutron) increased the intensity of protein catabolism and led to the attenuation of translation. The impact of IRs on protein synthesis and degradation was accompanied by rearrangements in energy metabolism and reallocation of nitrogen, probably due to enhanced protein catabolism. At least partially, those changes seem to fuel secondary metabolites production, including riboflavin, various phytoalexins, phytosiderophores, ferulic and sinapic acids, kaempferol, quercetin, nictoflorin, gallate, and podophyllotoxin. Many of these compounds have antioxidant or radioprotective properties. To focus on possible targets for gene editing, we identified genes differentially regulated after all types of IR exposure and potential transcription factors regulating secondary metabolism, including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC families.},
  author = {Volkova, Polina and Prazyan, Alexandr and Podlutskii, Mikhail and Saburov, Vyacheslav and Kazakova, Elizaveta and Bitarishvili, Sofia and Duarte, Gustavo T. and Shesterikova, Ekaterina and Makarenko, Ekaterina and Lychenkova, Maria and Ben, Cécile and Gentzbittel, Laurent and Kazakov, Evgenii and Moiseev, Alexandr and Diuzhenko, Sergei and Korol, Marina and Bondarenko, Ekaterina},
@@ -10706,6 +11045,22 @@ @article{wichers_common_2021
  year = {2021}
 }
 
+@article{wight_anthropogenic_2024,
+ author = {Wight, Jordan and Byrne, Alexander S. and Tahlan, Kapil and Lang, Andrew S.},
+ doi = {10.1128/aem.01809-23},
+ journal = {Applied and Environmental Microbiology},
+ keywords = {{\textgreater}UseGalaxy.eu},
+ month = {February},
+ note = {Publisher: American Society for Microbiology},
+ number = {3},
+ pages = {e01809--23},
+ title = {Anthropogenic contamination sources drive differences in antimicrobial-resistant {Escherichia} coli in three urban lakes},
+ url = {https://journals.asm.org/doi/full/10.1128/aem.01809-23},
+ urldate = {2024-06-07},
+ volume = {90},
+ year = {2024}
+}
+
 @article{wight_anthropogenic_2024,
  author = {Wight, Jordan and Byrne, Alexander S. and Tahlan, Kapil and Lang, Andrew S.},
  doi = {10.1128/aem.01809-23},
@@ -10741,6 +11096,24 @@ @article{williams_discovery_2023
  year = {2023}
 }
 
+@article{willnow_nuclear_2024,
+ abstract = {Histone acetylation regulates gene expression, cell function and cell fate1. Here we study the pattern of histone acetylation in the epithelial tissue of the Drosophila wing disc. H3K18ac, H4K8ac and total lysine acetylation are increased in the outer rim of the disc. This acetylation pattern is controlled by nuclear position, whereby nuclei continuously move from apical to basal locations within the epithelium and exhibit high levels of H3K18ac when they are in proximity to the tissue surface. These surface nuclei have increased levels of acetyl-CoA synthase, which generates the acetyl-CoA for histone acetylation. The carbon source for histone acetylation in the rim is fatty acid β-oxidation, which is also increased in the rim. Inhibition of fatty acid β-oxidation causes H3K18ac levels to decrease in the genomic proximity of genes involved in disc development. In summary, there is a physical mark of the outer rim of the wing and other imaginal epithelia in Drosophila that affects gene expression.},
+ author = {Willnow, Philipp and Teleman, Aurelio A.},
+ copyright = {2024 The Author(s)},
+ doi = {10.1038/s41586-024-07471-4},
+ issn = {1476-4687},
+ journal = {Nature},
+ keywords = {{\textgreater}UseGalaxy.eu, Cell proliferation, Differentiation},
+ language = {en},
+ month = {June},
+ note = {Publisher: Nature Publishing Group},
+ pages = {1--9},
+ title = {Nuclear position and local acetyl-{CoA} production regulate chromatin state},
+ url = {https://www.nature.com/articles/s41586-024-07471-4},
+ urldate = {2024-06-08},
+ year = {2024}
+}
+
 @article{winkler_contrast_2020,
  abstract = {Mass spectrometry imaging (MSI) enables the unbiased characterization of surfaces with respect to their chemical composition. In biological MSI, zones with differentialmass profiles hint towards localized physiological processes, such as the tissue-specific accumulation of secondary metabolites, or diseases, such as cancer. Thus, the efficientdiscovery of ‘regions of interest’ (ROI) is of utmost importance in MSI. However, often the discovery of ROIs is hampered by high background noise and artifact signals. Especially in ambient ionization MSI, unmasking biologically relevant information from crude data sets is challenging. Therefore, we implemented a Threshold Intensity Quantization (TrIQ) algorithm for augmenting the contrast in MSI data visualizations. The simple algorithm reduces the impact of extreme values (‘outliers’) and rescales the dynamic range of mass signals. We provide an R script for post-processing MSI data in the imzML community format (https://bitbucket.org/lababi/msi.r) and implemented the TrIQ in our open-source imaging software RmsiGUI (https://bitbucket.org/lababi/rmsigui/). Applying these programs to different biological MSI data sets demonstrated the universal applicability of TrIQ for improving the contrast in the MSI data visualization. We show that TrIQ improves a subsequent detection of ROIs by sectioning. In addition, the adjustment of the dynamic signal intensity range makes MSI data sets comparable.},
  author = {Winkler, Robert and Rosas-Román, Ignacio},